You should ask this in the Oracle forum but I'll give you something to try out first:
1) Modify your startup script to include the following properties:
-Xdebug
-Xnoagent
-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8000
2) Start the server (and deploy your application, if it isn't deployed already)
3) Point your IDE's debugger to the server's JVM by doing something like "Debug -> Enable Remote Debugging -> Attach..." and filling in the server's hostname and port (8000 in the example). Anyway, there must be a help page about debugging in JBuilder...